Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria

Casciotti, Karen L.; Ward, Bess B.

doi:10.1016/j.femsec.2004.11.002

Cited by 94 publications

(54 citation statements)

References 46 publications

(74 reference statements)

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“…The distribution of the radiatively active trace gas nitrous oxide (N 2 O) may also be strongly influenced by these organisms: AOB (Casciotti and Ward, 2005), denitrifiers, and now AOA (Hallam et al, 2006b) possess nitric oxide reductase (nor) genes that could be involved in N 2 O production. Anammox bacteria are now known to produce N 2 O as well (Kartal et al, 2007a) -not as an intermediate of the anammox reaction but apparently as a result of NO detoxification.…”

Section: New Paradigmsmentioning

confidence: 99%

New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation

2007

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Microbial activities drive the global nitrogen cycle, and in the past few years, our understanding of nitrogen cycling processes and the micro-organisms that mediate them has changed dramatically. During this time, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle. All available evidence indicates that these processes and organisms are critically important in the environment, and particularly in the ocean. Here we review what is currently known about the microbial ecology of anaerobic and archaeal ammonia oxidation, highlight relevant unknowns and discuss the implications of these discoveries for the global nitrogen and carbon cycles.

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Section: New Paradigmsmentioning

confidence: 99%

New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation

2007

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“…The other mechanism, known as nitrifier-denitrification, is the sequential reduction of NO − 2 to NO and then N 2 O by the action of the nitrite reductase (NIR, encoded by the gene nirK) and the nitric oxide reductase (NOR, encoded by the gene norB). All of the ammoniaoxidizing bacteria that have been screened to date contain the nirK and norB genes (Casciotti and Ward, 2001;Shaw et al, 2006;Casciotti and Ward, 2005;Cantera and Stein, 2007;Norton et al, 2008;Arp et al, 2007), and the conversion of 15 NO − 2 to 15 N 2 O has been demonstrated in several genera (Poth and Focht, 1985;Shaw et al, 2006). Archaeal ammonia oxidizers also appear to possess nirK and norB homologs (Treusch et al, 2005;Hallam et al, 2006;Walker et al, 2010) but it is not known whether the proteins encoded by these genes are involved in N 2 O production.…”

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confidence: 99%

Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

2010

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Abstract. Nitrous oxide (N 2 O) is a trace gas that contributes to the greenhouse effect and stratospheric ozone depletion. The N 2 O yield from nitrification (moles N 2 O-N produced per mole ammonium-N consumed) has been used to estimate marine N 2 O production rates from measured nitrification rates and global estimates of oceanic export production. However, the N 2 O yield from nitrification is not constant. Previous culture-based measurements indicate that N 2 O yield increases as oxygen (O 2 ) concentration decreases and as nitrite (NO − 2 ) concentration increases. Here, we have measured yields of N 2 O from cultures of the marine β-proteobacterium Nitrosomonas marina C-113a as they grew on low-ammonium (50 µM) media. These yields, which were typically between 4 × 10 −4 and 7 × 10 −4 for cultures with cell densities between 2×10 2 and 2.1×10 4 cells ml −1 , were lower than previous reports for ammonia-oxidizing bacteria. The observed impact of O 2 concentration on yield was also smaller than previously reported under all conditions except at high starting cell densities (1.5 × 10 6 cells ml −1 ), where 160-fold higher yields were observed at 0.5% O 2 (5.1 µM dissolved O 2 ) compared with 20% O 2 (203 µM dissolved O 2 ). At lower cell densities (2 × 10 2 and 2.1 × 10 4 cells ml −1 ), cultures grown under 0.5% O 2 had yields that were only 1.25-to 1.73-fold higher than cultures grown under 20% O 2 . Thus, previously reported many-fold increases in N 2 O yield with dropping O 2 could be reproduced only at cell densities that far exceeded those of ammonia oxidizers in the ocean. The presence of excess NO − 2 (up to 1 mM) in the growth medium also increased N 2 O yields by an average of 70% to 87% depending on O 2 concentration. We made stable

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“…S6 and Table S1 in the supplemental material). We acknowledge that the high specificity of reverse transcription (RT)-PCR assays may fail to detect related mRNA targets (in this case, expressed bacterial nirK and norB); nonetheless, the assay is broadly accepted as state of the art for assessing expression of genes involved in N 2 O production by denitrification pathways (11,15). Thus, we have assembled four independent lines of evidence that argue against the possibility that minor denitrifying bacterial populations in the enrichment are responsible for N 2 O production in the strain MY1 culture: (i) assays were clearly aerobic (ammonia oxidation and N 2 O production were impaired at reduced O 2 [see above]), (ii) the AFM had only NH 3 as an electron donor, (iii) an ammonia oxidation inhibitor (which does not inhibit denitrification) completely inhibited the production N 2 O, and (iv) neither of the two bacterial genes that might potentially participate in N 2 O production by Bacteria present in the coculture was expressed.…”

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confidence: 99%

Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

Jung

Park

Min

et al. 2011

Appl Environ Microbiol

243

222

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Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [ 13 C]bicarbonate assimilation assay showed stoichiometric incorporation of 13 C into Archaeaspecific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to "Candidatus Nitrosopumilus maritimus" revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N 2 O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated "Candidatus Nitrosoarchaeum koreensis."

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Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria

Cited by 94 publications

References 46 publications

New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation

New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation

Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

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